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PubMed1986

Scrotal circumference in yearling Hereford bulls: adjustment factors, heritabilities and genetic, environmental and phenotypic relationships with growth traits.

Field data on 4,233 yearling Hereford bulls were analyzed using fixed and mixed model least-squares procedures to examine factors affecting scrotal circumference; determine appropriate adjustment factors; and study genetic, environmental and phenotypic relationships among scrotal circumference and growth traits. Scrotal circumference was affected by postweaning feed level; contemporary group/feed level; age of dam; and covariates age, weight and height. Of the three covariates, weight had the greatest effect, and any factor which caused an increase in weight tended to increase scrotal circumference. Quadratic effects of age, weight, height and age X age of dam interaction effects were significant or approached significance, but were of minor importance. Large contemporary group effects suggested the need for expressing scrotal circumferences as trait ratios or as deviations from contemporary group means. Scrotal circumference adjustment factors recommended for yearling Hereford bulls were .026 cm X d-1 of age and .8, .2 and .1 for sons of 2-, 3- and 4-yr old dams, respectively. Heritability of weight-adjusted scrotal circumference was .46 +/- .06 compared with .49 +/- .06 for age-adjusted scrotal circumference, indicating considerable additive genetic variation for relative scrotal size. Correlations between scrotal circumference and growth traits were moderate to high. The genetic correlation between scrotal circumference and yearling weight was the highest of these at .44 +/- .16. Potential implications of this relationship are discussed.

Animals↗
PubMed1996

Phenotypic and phylogenetic analyses show Microcoleus chthonoplastes to be a cosmopolitan cyanobacterium.

We used micromanipulation to isolate from their environment representative samples of seven geographically distant field populations fitting the description of Microcoleus chthonoplastes (a cyanobacterium) and obtained seven corresponding cultured strains. Samples of both field populations and cultures were phenotypically characterized by microscale techniques, and their partial 16S rRNA gene sequences were compared by denaturing gradient gel electrophoresis and in some cases by sequencing. All field populations and strains were phenotypically extremely coherent, and their 16S rRNA sequences were indistinguishable by DGGE. The sequences determined were identical or virtually identical. Thus, M. chthonoplastes represents a single, well-delimited taxon with a truly cosmopolitan distribution. Comparison with three culture collection strains originally assigned to M. chthonoplastes revealed that strain PCC 7420 belongs to the same tightly delimited group, both phenotypically and in 16S rRNA gene sequence, but that strains SAG 3192 and 10mfx do not.

Base Sequence↗
PubMed1999

A Sabin vaccine-derived field isolate of poliovirus type 1 displaying aberrant phenotypic and genetic features, including a deletion in antigenic site 1.

Poliovirus strains derived from the oral poliovirus vaccine (Sabin) can be differentiated from wild-type poliovirus by tests based on either immunological or genetic properties of the strains. The characterization of a recently identified poliovirus type 1 isolate with exceptional properties is described. Initial phenotypic analysis of the virus by use of polyclonal absorbed antisera suggested a wild-type character. However, the different genomic analyses all confirmed the Sabin-derived character of the virus. All 17 plaques isolated from the strain shared these properties, thus excluding the possibility of a mixture of a wild-type and a Sabin-derived strain. To elucidate the properties of this virus further, the nucleotide sequences of the P1 region and most of the 5' non-coding region were established. Although the nucleotide identity with Sabin 1 was more than 99.4%, mutations were observed in regions encoding three major antigenic sites; the deduced amino acid substitutions confirmed the aberrant results of micro-neutralization assays with site-specific monoclonal antibodies. The most striking feature was the existence of a hexanucleotide deletion in the VP1 gene, which gave rise to a two amino acid deletion in the BC loop. In spite of these antigenic changes, the strain was readily serotyped as poliovirus type 1 under standard conditions. Likewise, replication of the virus under cell culture conditions was not affected by these mutations or by the deletion. Standard polio vaccination protects against this aberrant virus, and its epidemiological significance remains open.

Amino Acid Sequence↗
PubMed2003

Enabling inverse metabolic engineering through genomics.

Inverse metabolic engineering (IME) is a powerful framework for engineering cellular phenotypes. Progress in this field has been limited by a lack of comprehensive methods for efficiently identifying the genetic basis of relevant phenotypes. Advances in genomics technologies, including DNA microarrays and gene sequencing, have dramatically improved our ability to relate changes in phenotype with associated changes in genotype. When applied in the context of IME, these tools should enable the integration of "evolutionary" and "direct" approaches to engineering cell physiology, which should improve our understanding of the complex interactions affecting the expression, evolution and engineering of traits in natural and industrial hosts.

Bacteria↗
PubMed1994

Phenotypic and genotypic diversity of fluorescent pseudomonads isolated from field-grown sugar beet.

A sample of 30 fluorescent pseudomonads isolated from the phyllosphere of sugar beet throughout a single growing season and shown to be closely related on the basis of fatty acid methyl ester (FAME) analysis was subjected to detailed phenotypic and genotypic characterization. Phenotypic traits were assessed on the basis of biochemical properties, assimilation of sole carbon sources, FAME analysis, organic pyrolysate content (MS-pyrolysis), and total cellular protein profiles. With the exception of total cellular protein profiles, numerical analysis of the data revealed two main clusters, each of which was divided into several subclusters. Numerical analysis of total cellular protein data failed to differentiate isolates into two main clusters, but nevertheless grouped isolates into six subclusters. On the basis of biochemical and carbon source assimilation profiles, 19 isolates were identified as Pseudomonas fluorescens biovar V, eight isolates as P. fluorescens biovar III and three isolates as P. syringae pathovar syringae. In general, all methods of phenotypic analysis grouped isolates according to time of sampling and leaf type. Genome analysis was undertaken by pulsed-field gel electrophoresis (PFGE) of PacI, SpeI, SwaI and XbaI macrorestriction fragments and revealed the presence of eight distinct genomic (clonal) groups. These groups correlated closely with the clusters generated by numerical analysis of phenotypic data, but there was no correlation between macrorestriction fragment profile and isolate identification; in fact the variation in macrorestriction fragment patterns within P. fluorescens biovars was as great as the variation detected between biovars, and between P. fluorescens and P. syringae. Statistical evaluation of macrorestriction fragment patterns revealed two examples of recent strain divergence: one was due to the presence of a 400 kbp plasmid within one isolate of a collection of nine otherwise genomically identical isolates, and the other was observed between two phenotypically similar isolates sampled 220 d apart. Genetic variation was expressed in terms of nucleotide diversity (pi) and pairwise comparisons yielded values ranging from 0.0029 to 0.1517. The mean intrapopulation genetic variation was high (0.0993), but limited genetic variation was detected among isolates sampled on each occasion. Taken together this suggests a population comprised of a variety of apparently distantly related clones (genomic groups), each adapted to local conditions. Genome sizes were estimated from the sum of SpeI restriction fragments and ranged from 4.2 to 5.5 Mbp. Examination of the distribution of XbaI, SpeI, SwaI and PacI restriction endonuclease sites showed that the distribution of SpeI sites differed significantly from the expected (random) distribution.

Bacterial Proteins↗
PubMed2001

Prevalence and mechanisms of macrolide resistance in Streptococcus pyogenes in Santiago, Chile.

Thirty-two macrolide-resistant Streptococcus pyogenes isolates were found among 594 clinical isolates collected from 1990 to 1998 in Santiago, Chile, for an overall prevalence of 7.2%. Among the 32 resistant isolates, 28 (87.5%) presented the M phenotype and 4 (12. 5%) presented the MLS(B) phenotype. Serotyping and pulsed-field gel electrophoresis analysis showed genetic diversity among the resistant isolates.

Anti-Bacterial Agents↗
PubMed1982

Genetic, phenotypic and environmental correlations among performance traits estimated from Limousin field data.

Field records from the North American Limousin Foundation performance testing program provided three data sets for the estimation of genetic, phenotypic and environmental correlations among several performance traits. The traits were: birth weight, preweaning average daily gain, adjusted 205-d weaning weight, postweaning average daily gain, adjusted 365-d yearling weight, weight/d of age, preweaning relative growth and postweaning relative growth. Birth weight had a positive genetic relationship with all measures of growth except pre- and postweaning relative growth. The genetic relationship between preweaning relative growth and birth weight was small and negative. Postweaning relative growth had little genetic relationship to birth weight. The genetic relationships among the various growth characteristics were positive, except for those involving pre- and postweaning relative growth. Postweaning relative growth was negatively associated with preweaning average daily gain and adjusted 205-d weight. Preweaning relative growth had little genetic association with adjusted 205-d weight, adjusted 365-d weight or weight/day of age.

Animals↗
PubMed2004

Genotypic and phenotypic diversity of Lactobacillus delbrueckii subsp. lactis strains of dairy origin.

Eighty-nine strains of Lactobacillus delbrueckii subsp. lactis isolated from Italian hard and semi-hard cheeses and artisan starter cultures were characterised by phenotypic and genotypic methods. Phenotypic diversity was evaluated by studying biochemical characteristics (i.e. acidifying and peptidase activities) of technological interest. Genotypic diversity was evidenced by RAPD-PCR and pulsed field gel electrophoresis (PFGE). Phenotypic characterisation indicated a wide variability of the acidifying activity within Lact. delbrueckii subsp. lactis. Although the data was variable, it allowed us to evidence groups of strains with different acidifying properties, especially in terms of acidification intensity. Concerning peptidase activity, Lact. delbrueckii subsp. lactis showed a homogeneously high x-prolil-dipeptidil-aminopeptidase activity and a considerable but more heterogeneous lysil-aminopeptidase activity. The increased resolution obtained by the use of two molecular typing techniques, i.e. RAPD-PCR and PFGE, allowed to widen the level of strain heterogeneity. Technological and ecological pressures are determinant in selecting Lact. delbrueckii subsp. lactis sub-populations which are more functional to the different cheese technologies.

Cheese↗
PubMed2007

Computational approaches to phenotyping: high-throughput phenomics.

The recent completion of the Human Genome Project has made possible a high-throughput "systems approach" for accelerating the elucidation of molecular underpinnings of human diseases, and subsequent derivation of molecular-based strategies to more effectively prevent, diagnose, and treat these diseases. Although altered phenotypes are among the most reliable manifestations of altered gene functions, research using systematic analysis of phenotype relationships to study human biology is still in its infancy. This article focuses on the emerging field of high-throughput phenotyping (HTP) phenomics research, which aims to capitalize on novel high-throughput computation and informatics technology developments to derive genomewide molecular networks of genotype-phenotype associations, or "phenomic associations." The HTP phenomics research field faces the challenge of technological research and development to generate novel tools in computation and informatics that will allow researchers to amass, access, integrate, organize, and manage phenotypic databases across species and enable genomewide analysis to associate phenotypic information with genomic data at different scales of biology. Key state-of-the-art technological advancements critical for HTP phenomics research are covered in this review. In particular, we highlight the power of computational approaches to conduct large-scale phenomics studies.

Computational Biology↗
PubMed1993

Genes necessary for expression of a virulence determinant and for transmission of Plasmodium falciparum are located on a 0.3-megabase region of chromosome 9.

Virulence of the human malaria parasite Plasmodium falciparum is believed to relate to adhesion of parasitized erythrocytes to postcapillary venular endothelium (asexual cytoadherence). Transmission of malaria to the mosquito vector involves a switch from asexual to sexual development (gametocytogenesis). Continuous in vitro culture of P. falciparum frequently results in irreversible loss of asexual cytoadherence and gametocytogenesis. Field isolates and cloned lines differing in expression of these phenotypes were karyotyped by pulse-field gel electrophoresis. This analysis showed that expression of both phenotypes mapped to a 0.3-Mb subtelomeric deletion of chromosome 9. This deletion frequently occurs during adaptation of parasite isolates to in vitro culture. Parasites with this deletion did not express the variant surface agglutination phenotype and the putative asexual cytoadherence ligand designated P. falciparum erythrocyte membrane protein 1, which has recently been shown to undergo antigenic variation. The syntenic relationship between asexual cytoadherence and gametocytogenesis suggests that expression of these phenotypes is genetically linked. One explanation for this linkage is that both developmental pathways share a common cytoadherence mechanism. This proposed biological and genetic linkage between a virulence factor (asexual cytoadherence) and transmissibility (gametocytogenesis) would help explain why a high degree of virulence has evolved and been maintained in falciparum malaria.

Agglutination↗
PubMed2005

Patient acceptability of genotypic testing for hemochromatosis in primary care.

PURPOSE: Genetic screening can enable timely detection and treatment of hereditary hemochromatosis (HH). Little is known about patient acceptability of DNA testing as compared to conventional phenotypic testing. METHODS: Within the HEIRS Study, a large primary-care screening study of HH and iron overload, we randomly assigned participants to receive brief information on either HH genotypic or phenotypic testing, and assessed the willingness to accept this test. The study was designed to recruit an equal number of African Americans and Caucasians. RESULTS: A total of 2500 participants were recruited from waiting rooms of primary care practices; 2165 participants who self-identified as African Americans and Caucasians were included in the analyses. Overall, 56% had accepted a genotypic test versus 58% for a phenotypic test. Adjusting for Field Center (FC), age, gender, race, educational attainment, global health rating, and knowledge of the test, the odds ratio of accepting a genotypic versus phenotypic test was 0.85 (95% CI: 0.71, 1.02; P = 0.078). Characteristics associated with test acceptance were age 45-64 years, female gender, Caucasian race, self-rated health less than ''very good'', and knowledge of the test. Test acceptance was associated with interest in knowing more about health (81%) and in helping family members (71%). Refusal reasons included a need to talk with a doctor (44%), concern about privacy (32%), and dislike of blood drawing (29%). CONCLUSION: In this diverse sample of primary care patients, stated acceptance of genotypic testing for HH mutations was similar to phenotypic testing for blood iron. Patient education regarding the nature of test, importance of disease detection, and privacy protection appear to be essential for achieving high rates of screening participation.

Adult↗
PubMed1997

Identification of Serpulina species associated with porcine colitis by biochemical analysis and PCR.

A PCR system for the detection and identification of group IV spirochetes (Serpulina pilosicoli) was designed to complement biochemical tests, e.g., the hippurate hydrolysis and beta-glucosidase tests, and to verify the accuracy of a previously proposed biochemical classification system. The PCR assay was based on amplification of a segment of the 16S rRNA gene. Both primers were constructed to selectively amplify the 16S rRNA gene of Serpulina pilosicoli. All analyzed Serpulina strains exhibiting the capacity to hydrolyze hippurate and lacking beta-glucosidase activity, including the type strain for spirochetal diarrhea, P43, were amplified with the PCR system. All other tested strains, including type and field strains of different phenotypes of Serpulina species, as well as Salmonella species, Campylobacter species, and Escherichia coli strains, were negative in the assay. Among the tested strains were 18 Scottish field isolates originating from the mucosae of pigs with colitis. A simple classification scheme, suitable for routine classification of porcine intestinal spirochetes, is also presented. The scheme is based on hemolysis, indole production, and the hippurate hydrolysis test.

Animals↗
PubMed1999

Characterization of Malassezia species by means of phenotypic characteristics and detection of electrophoretic karyotypes by pulsed-field gel electrophoresis (PFGE).

A total of 220 isolates of the genus Malassezia obtained from affected skin of animals and humans were included in this study. The isolates were examined for their belonging to the known species Malassezia pachydermatis, Malassezia sympodialis, Malassezia furfur, Malassezia obtusa, Malassezia restricta, Malassezia globosa and Malassezia slooffiae by means of phenotypic and biochemical characteristics as well as their ability to assimilate polyethylen(20)-sorbitan-esters (Tween 20, 40, 60, 80). The electrophoretic karyotypes of all isolates were studied by pulsed-field gel electrophoresis. Of the 220 Malassezia isolates examined, 217 were identified as M. pachydermatis and three were classified as M. sympodialis. Moreover, the proof of limited lipid-dependence of M. pachydermatis indicated that the commonly used criterion 'lipid-independence' is not sufficient to differentiate this species from the other known Malassezia species.

Animals↗
PubMed1996

Field effect of human colon carcinoma on normal mucosa: relevance of carcinoembryonic antigen expression.

Human colon cancer usually develops on a mucosa which has already undergone multiple steps of genetic change. These multiple steps create a field effect characterized by the presence of morphologically normal, but biologically altered epithelial cells. This aims of this study were to evaluate whether the expression of carcinoembryonic antigen (CEA) can act as a phenotypic marker of the field effect, and to map its topography in relation to the presence of colorectal adenocarcinoma. The expression of CEA was tested by immunohistochemistry on morphologically normal mucosa at 4 increasing distances from 14 autologous cases of colorectal adenocarcinoma. CEA expression in the normal mucosa was compared to the tumor. The results show that in the mucosa adjacent to the edge of the autologous tumor, CEA is expressed to the same level as displayed in the carcinoma; there is a decrease in CEA expression in normal mucosa located at 1 cm or more from the edge of carcinoma. Mucosa sampled at 5 and 10 cm from the tumor expresses CEA at the same low level as in mucosa of control subjects with no colorectal neoplasm. In conclusion, this study demonstrates a gradient of CEA expression in the peritumoral area, supporting the concept of field effect, and maps its extent. These data are relevant to the biology of human colorectal cancer, and more practically, to the optimal location of surgical resection.

Antibodies, Monoclonal↗
PubMed2003

Genotypic and phenotypic properties of coagulase-negative staphylococci causing dialysis catheter-related sepsis.

Sixty coagulase-negative staphylococcus (CNS) isolates were recovered from the blood cultures or peritoneal dialysate effluent of 43 patients on renal dialysis. The patients had either renal dialysis catheter-related sepsis (CRS) or continuous ambulatory peritoneal dialysis (CAPD)-associated peritonitis. Isolates were characterized by biotyping, and genotyped by pulsed-field gel electrophoresis (PFGE). Phenotypic properties of the strains were also investigated. Several genotypes were identified with no one specific strain of CNS being associated with CRS. However, closely related strains were isolated from several patients within the units studied, suggesting horizontal transfer of micro-organisms. Genotypic macro-restriction profiles did not concur with phenotypic profiles or biotypes, confirming that genotyping is required for epidemiological studies. All staphylococcal strains were investigated for the production of phenotypic characteristics. Significant differences were predominantly seen in the production of lipase, esterase and elastase in strains isolated from the renal patients with CRS and CAPD-associated peritonitis, compared with a non-septic control group. These phenotypic characteristics may therefore have a role in the maintenance of CRS in renal patients.

Adult↗
PubMed1994

Variations in ploidy among isolates of Botrytis cinerea: implications for genetic and molecular analyses.

Field isolates and laboratory strains of Botrytis cinerea, an ascomycetous fungus causing considerable economic losses, e.g., as "grey mould" of vine, were compared for differences in ploidy level by determining their DNA content per nucleus. Strain SAS56, an ascospore line used routinely for genetic analyses, is probably polyploid, since treatment with benomyl causes a significant reduction in DNA content per nucleus. This conclusion is substantiated by the increased sensitivity of the putative haploid derivatives to mutagens (UV and EMS). Molecular analyses (RAPD) of the haploidized strains indicate a very limited degree of heterozygosis of the parent strain SAS56. Analysis of field isolates of B. cinerea showed that their DNA content per nucleus varied considerably, indicating that aneuploidy/polyploidy is a widespread phenomenon in this species. This can explain both the variability and phenotypic instability of many field isolates of this fungus and the unusual difficulties faced by researchers in recovering stable recessive laboratory mutants. Since the haploid derivatives of SAS56 resemble the parent strain in their parasitic and physiological properties they should provide a good basis for classical and molecular genetic studies.

Base Sequence↗
PubMed2005

Antimicrobial-drug susceptibility of human and animal Salmonella typhimurium, Minnesota, 1997-2003.

We compared antimicrobial resistance phenotypes and pulsed-field gel electrophoresis (PFGE) subtypes of 1,028 human and 716 animal Salmonella enterica serotype Typhimurium isolates from Minnesota from 1997 to 2003. Overall, 29% of human isolates were multidrug resistant. Predominant phenotypes included resistance to ampicillin, chloramphenicol or kanamycin, streptomycin, sulfisoxazole, and tetracycline (ACSSuT or AKSSuT). Most human multidrug-resistant isolates belonged to PFGE clonal group A, characterized by ACSSuT resistance (64%), or clonal group B, characterized by AKSSuT resistance (19%). Most animal isolates were from cattle (n = 358) or swine (n = 251). Eighty-one percent were multidrug resistant; of these, 54% were at least resistance phenotype ACSSuT, and 43% were at least AKSSuT. More than 80% of multidrug-resistant isolates had a clonal group A or B subtype. Resistance to ceftriaxone and nalidixic acid increased, primarily among clonal group A/ACSSuT isolates. Clonal group B/AKSSuT isolates decreased over time. These data support the hypothesis that food animals are the primary reservoir of multidrug-resistant S. Typhimurium.

Animals↗